HaploVar: Defining Local Haplotype Variants for Use in Trait Associationand Trait Prediction Analyses
A local haplotyping tool for use in trait association and trait prediction analyses pipelines. 'HaploVar' enables users take single nucleotide polymorphisms (SNPs) (in VCF format) and a linkage disequilibrium (LD) matrix, calculate local haplotypes and format the output to be compatible with a wide range of trait association and trait prediction tools. The local haplotypes are calculated from the LD matrix using a clustering algorithm called density-based spatial clustering of applications with noise ('DBSCAN') (Ester et al., 1996) <ISBN: 1577350049>.
| Version: | 0.1.1 |
| Depends: | R (≥ 4.00) |
| Imports: | dplyr,tidyr,tibble,magrittr,dbscan |
| Suggests: | knitr,rmarkdown |
| Published: | 2025-07-21 |
| DOI: | 10.32614/CRAN.package.HaploVar |
| Author: | Tessa MacNish [aut, cre], Hawlader Al-Mamun [ctb], Thomas Bergmann [ctb], Mitchell Bestry [ctb], Jacob Marsh [ctb], David Edwards [ctb] |
| Maintainer: | Tessa MacNish <tessa.macnish at research.uwa.edu.au> |
| License: | MIT + fileLICENSE |
| NeedsCompilation: | no |
| CRAN checks: | HaploVar results |
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